Journal of Biomolecular Structure and Dynamics, 2016 Feb;34(2):376-383.
Role of acidic domain of α-synuclein in amyloid fibril formation: A molecular dynamics study
SeongByeong Parka, Jeseong Yoona, Soonmin Jangb, Kyunghee Leeb and Seokmin Shina*
aDepartment of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea; bDepartment of Chemistry, Sejong University, Seoul 143-747, Republic of Korea
A detailed mechanism of the pathology of α-synuclein in the Parkinson’s disease has not been clearly known. Recent studies suggested possible chaperone-like role of the acidic C-terminal region of α-synuclein during the amyloid formation. It was found that the α-synuclein fiber formation is accelerated by mutations of proline residues to alanine. We performed replica exchange molecular dynamics (REMD) simulations on the acidic and NAC domains for the wild type and proline-to-alanine mutants of α-synuclein under various conditions. Our results showed that the structural changes induced by either a pH change or an introduction of the mutation lead to the reduction of mutual contacts between the NAC and the acidic regions. These results suggest that the highly charged acidic region of α-synuclein may act as an intramolecular chaperone by protecting the hydrophobic domain from aggregation. Understanding the function of such chaperone-like parts of fibril-forming proteins is expected to provide novel insights into the mechanism of amyloid formation.
KEYWORDS: amyloid formation; intramolecular chaperone; molecular dynamics; protein aggregation; α-synuclein
Misfolded proteins, whose structures are disordered in normal conditions, can lead to the formation of aggregates. Understanding the mechanism of such aggregation is very important to elucidate possible causes for various neurodegenerative disorders such as Alzheimer’s, prion, or Parkinson’s diseases. Alzheimer amyloid b-peptide and Parkinson’s synuclein protein are the most well-known examples of such cases. Conventional experimental methods such as X-ray and NMR have limitations to examine the structural properties of such ‘intrinsically unstructured’ proteins, although recent advances such as solid state NMR produce some clues to the characteristics of them. Computational approaches can provide useful information of the structural properties of ‘intrinsically unstructured’ proteins and the mechanism of aggregation of such proteins. Recent advances in computational capabilities and efficient conformational search methods such as various versions of replica exchange (or parallel tempering) simulation methods allow us to tackle challenging problems like elucidation of aggregation mechanism of misfolded proteins.
In contrast to the Aβ peptide, α-synuclein, as an amyloid forming protein, has a rather long sequence consisting of three different domains. The three domains exhibit different characters: the membrane-binding N-terminal region is amphipathic, the NAC domain is hydrophobic, and the polar C-terminal tail is acidic. The middle sequence of the hydrophobic NAC domain is usually considered to be important for the aggregation of α-synuclein. While the N-terminal region is known to form α-helices bound on the membrane, the acidic C-terminal region is unstructured. The possible role of the acidic region during the amyloid formation of α-synuclein is generally unknown. Recent experiments have provided interesting results suggesting that structural changes in the acidic region may affect the aggregation processes. Most notably, lowering the pH or the mutation of proline residues to alanine residues in the acidic region accelerates the aggregation kinetics.
α-Synuclein is a 140-residue protein primarily found in presynaptic terminals. In solution, it exists as an intrinsically disordered or naturally unfolded protein. α-Synuclein is present as fibrillar aggregates of Lewy bodies, a pathological hallmark of the Parkinson’s disease, but the detailed mechanism of its pathology has not been known. Y. Engelborghs et. al. reported FK506 binding proteins accelerate the fibril formation of wild type α-Synuclein, and the P(108,117,120,128,138)A mutation facilitates the aggregation process (1,2). In the present study, we performed systematic simulations of α-synuclein under various conditions in order to elucidate structural characteristic of the acidic region responsible for the changes in aggregation behavior.
The radius of gyration as a function of temperature for the wild type and P-to-A mutant of the acidic domain showed that the removal of proline residues makes the acidic domain more flexible than the wild-type α-synuclein. It was also shown that the radius of gyration of the combined sequence of the NAC (nonamyloid component domain, residue 61-100) and acidic domain (residue 101-140) was larger than that of the wild-type α-synuclein (Figure 1). This difference can be mainly attributed to the increase in the relative distance between the two regions as a result of the reduction in rigidity of the acidic region after the removal of proline residues.
Figure 1. Radius of gyration as a function of temperature and representative configurations for the wild type and P-to-A mutant of (a) the acidic region alone and (b) the combined sequence of the NAC and acidic region under the neutral condition and the acidic condition of pH=2.
Our results suggested that the restricted cis-trans isomerization of the proline residue in the acidic domain would make the acidic domain less flexible and protect the NAC from other monomers of α-Synuclein. One may argue that the natural role of the acidic region is to prevent the aggregation of the hydrophobic NAC domain and maintain the functional form of α-synuclein. The present study showed that mutations of the proline residues to alanine make the acidic region much more flexible and the increased flexibility prevents the C-terminal domain from maintaining close contact with the NAC domain. As a result, the acidic C-terminal region can no longer protect the NAC domain from interacting with other chains for aggregation (Figure 2).
Figure 2. Schematic picture showing structural changes in the acidic region due to P-to-A mutant and their influences on the possible interactions between the NAC and acidic regions.
Recently, we also performed the classical MD simulations on the oligomers based on the newly published structures of α-Synuclein (3). Our results showed that the P(108, 117, 120, 128, 138)A mutation could make the NAC less exposed to solvent and the hydrophobicity of the NAC get increased as the aggregation proceeded (Figure 3). It can be argued that the inflexibility of the proline in the acidic domain could play a chaperon-like role in the aggregation process.
Figure 3. (a) Time evolution of numbers of water around the NAC for α-Synuclein tetramers. (b) Time evolution of numbers of water around the NAC per monomer for different α-Synuclein oligomers.
The importance of this study is two-fold. First, the results of the present study are expected to provide plausible scenarios for the role of the acidic region in the prevention of amyloid formation of α-synuclein. In particular, our results suggest that the acidic C-terminal region may act as an “intramolecular chaperone”, which keeps α-synuclein from aggregating under normal conditions. Understanding the function of such chaperone-like parts of fibril-forming proteins is expected to provide novel insights into the mechanism of amyloid formation and provide new treatment courses for diseases caused by protein aggregation. Second, our results from the related studies also suggested that amyloid formation is basically a hierarchical process and different topologies for on-the-pathway intermediates are favored in the different stages of aggregation (Figure 4). Computational studies such as the present work are expected to play an important role to provide fundamental understanding for such structural changes and ultimately the detailed mechanism of amyloid formation, which will be the subject of our future works.
Figure 4. Schematic picture illustrating hierarchical processes and important species involved in the amyloid formation.
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(2) Meuvis, J.; Gerard, M., Desender, L., Baekelandt, V., Engelborghs, Y. (2010) The Conformation and the Aggregation Kinetics of α-Synuclein Depend on the Proline Residues in Its C-Terminal Region. Biochemistry 49 (43): 9345-9352.
(3) Tuttle, M. D., Comellas, G., Nieuwkoop, A. J., Covell, D. J., Berthold, D. A., Kloepper, K. D., Courtney, J. M., Kim, J. K., Barclay, A. M., Kendall, A., Wan, W., Stubbs, G., Schwieters, C. D., Lee, V. M. Y., George, J. M., Rienstra, C. M. (2016) Solid-state NMR structure of a pathogenic fibril of full-length human α -synuclein. Nat. Struct. Mol. Biol. 23 (5): 409-415.
Acknowledgements: This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (MSIP): No.2007-0056095 (CMD), No.2012M3C1A6035358 (EDISON) and No.2012M3A9D1054622 (BIT).
Seokmin Shin, Ph.D.
Professor and Chair
Department of Chemistry
College of Natural Sciences
Seoul National University
Seoul 08826, Korea